72 lines
2.9 KiB
Groovy
72 lines
2.9 KiB
Groovy
// This file is based on the nf-core/tools pipeline-template.
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// Changes to this file must be propagated via wf-template.
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class WorkflowMain {
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// Citation string for pipeline
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public static String citation(workflow) {
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return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
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"* The nf-core framework\n" +
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" https://doi.org/10.1038/s41587-020-0439-x\n\n"
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}
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// Generate help string
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public static String help(workflow, params, log) {
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String line_sep = ' \\ \n\t'
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String command_example = params.wf.example_cmd.join(line_sep)
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String command = 'nextflow run ' + workflow.manifest.name + line_sep + command_example
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String help_string = ''
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help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs)
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help_string += NfcoreSchema.paramsHelp(workflow, params, command)
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help_string += '\n' + citation(workflow) + '\n'
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return help_string
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}
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// Generate parameter summary log string
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public static String paramsSummaryLog(workflow, params, log) {
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String workflow_version = NfcoreTemplate.version(workflow)
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String summary_log = ''
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summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs)
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summary_log += NfcoreSchema.paramsSummaryLog(workflow, params)
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summary_log += '\n' + citation(workflow) + '\n'
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summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs)
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summary_log += "\nThis is ${workflow.manifest.name} ${workflow_version}.\n"
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summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs)
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return summary_log
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}
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// Validate parameters and print summary to screen
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public static void initialise(workflow, params, log) {
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// Print help to screen if required
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if (params.help) {
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log.info help(workflow, params, log)
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System.exit(0)
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}
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// Print workflow version and exit on --version
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if (params.version) {
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String workflow_version = NfcoreTemplate.version(workflow)
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log.info "${workflow.manifest.name} ${workflow_version}"
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System.exit(0)
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}
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// Explode on conda
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// conda.enabled seems to be backward compatible but wrap this
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// in a generic catch just in case
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try {
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if (workflow.session.config.conda.enabled) {
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log.error "Sorry, this workflow is not compatible with Conda, please use -profile standard (Docker) or -profile singularity."
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System.exit(1)
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}
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} catch(Exception e) {}
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// Validate workflow parameters via the JSON schema
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if (params.validate_params) {
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NfcoreSchema.validateParameters(workflow, params, log)
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}
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// Print parameter summary log to screen
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log.info paramsSummaryLog(workflow, params, log)
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}
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}
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